combineRIP: Combined predictions from (presumably) biological replicates.

In yueli-compbio/RIPSeeker: RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

Description

A simple helper function that combines multiple prediction lists from biological replicates into a single list.

Usage

combineRIP(ripPath, pattern="gff3$", 
	combineOption="intersect", 
	pvalCutoff=1, pvalAdjCutoff=1, eFDRCutoff=1, 
	logOddCutoff=-Inf, maxgap=1e3, minIntersect, genomeBuild)

Arguments

ripPath	Path to predictions list in a select format as indicated by the file extension.
pattern	Pattern for the names of the prediction files to combine. The file names are expected to have a common extension such as "bed", "gff3", "gtf", but this is not enforced. Default: "gff3$" (i.e. the default output RIPregions.gff3 from ripSeek).
combineOption	Options on how to combine the peaks including: "intersect": is selected (default), only peaks in each biological replicate list that overlap with or are adjacent within maxgap nucleotides to at least minIntersect other replicates will be kept. If minIntersect is unspecified, then only the peaks that consistently predicted in all replicates are kept. "merge": All overlapping peaks from the replicates will be merged into one peak. "union": All overlapping peaks from the replicates will be merged into one peak.
pvalCutoff	Threshold for the p-value cutoff. Only peaks with p-value less than the logOddCutoff will be reported. Default: 1 (i.e. no cutoff).
pvalAdjCutoff	Threshold for the adjusted p-value cutoff. Only peaks with adjusted p-value less than the logOddCutoff will be reported. Default: 1 (i.e. no cutoff).
eFDRCutoff	Threshold for the empirical false discovery rate (eFDR). Only peaks with eFDR less than the eFDRCutoff will be reported. Default: 1 (i.e. no cutoff).
logOddCutoff	Threshold for the log odd ratio of posterior for the RIP over the background states (See seekRIP). Only peaks with logOdd score greater than the logOddCutoff will be reported. Default: -Inf (i.e. no cutoff).
maxgap	Maximum gap allowed to determine two peaks agree with each other.
minIntersect	Mininum number of replicates required to have peaks either intersect or are adjacent to the peak in other replciate.
genomeBuild	Genome build used to obtain the chromosome information from online UCSC database to assign chromosome length to the GRanges object created as the combined peak list.

Value

gr	GRanges object containning chromosome locations of the combined peaks.

Note

Please run ripSeek first on all biological replicates and renamed each "RIPregions.gff3" output to correspond to different biological replicates and place all of the files into a single folder. The path of this folder can then be used as the input argument for ripPath.

Author(s)

Yue Li

References

P. Aboyoun, H. Pages and M. Lawrence. GenomicRanges: Representation and manipulation of genomic intervals. R package version 1.8.9.

Michael Lawrence, Vince Carey and Robert Gentleman. rtracklayer: R interface to genome browsers and their annotation tracks. R package version 1.16.3.

See Also

combineAlignGals, ripSeek, import, import, reduce, countOverlaps

Examples

# Retrieve system files
ripPath <- system.file("extdata/RIPregions", package="RIPSeeker")

gr1 <- combineRIP(ripPath, combineOption="intersect", genomeBuild="mm9")

gr2 <- combineRIP(ripPath, combineOption="merge", genomeBuild="mm9")

gr3 <- combineRIP(ripPath, combineOption="union", genomeBuild="mm9")

length(gr1)

length(gr2)

length(gr3)

yueli-compbio/RIPSeeker documentation built on May 8, 2019, 2:34 a.m.